def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: the response
"""
# get a properly formatted newick tree with branch lengths
T, B, N = FtreeIO.newick_to_TBN(fs.tree)
# get the vertex valuations
all_valuations = TB_to_harmonic_valuations(T, B)
valuations = all_valuations[fs.first_index:]
nfigures = (fs.last_index - fs.first_index) + 1
# do the layout
if fs.equal_arc_layout:
v_to_location = FtreeAux.equal_arc_layout(T, B)
elif fs.equal_daylight_layout:
v_to_location = FtreeAux.equal_daylight_layout(T, B, 3)
# draw the image
physical_size = (fs.width, fs.height)
tikzpicture = DrawEigenLacing.get_forest_image_ftree(
T, B, N, v_to_location,
physical_size, valuations, nfigures, fs.inner_margin,
fs.reflect_trees, fs.show_vertex_labels, fs.show_subfigure_labels)
packages = []
preamble = '\\usetikzlibrary{snakes}'
return tikz.get_figure_response(
tikzpicture, fs.tikzformat, g_figure_caption, g_figure_label,
packages, preamble)
def get_response_content(fs):
# get a properly formatted newick tree with branch lengths
tree_string = '((1:1, 2:1)6:1, 3:1, (4:1, 5:1)7:1)8;'
tree = Newick.parse(tree_string, SpatialTree.SpatialTree)
# get the fiedler-like vertex valuation
fiedler = [1, 1, -1, -1, -1, 1, -1, -1]
# create a node id map
ids = [None]*8
for node in tree.preorder():
index = int(node.name) - 1
ids[index] = id(node)
# convert fiedler into a dictionary
v1 = dict((ids[i], float(fiedler[i])) for i in range(8))
# convert the annotations into dictionaries
v2s = [dict((ids[i], float(v[i])) for i in range(8)) for v in g_annotation]
# do the layout
try:
layout = FastDaylightLayout.StraightBranchLayout()
layout.do_layout(tree)
except RuntimeError as e:
pass
# draw the image
try:
ext = Form.g_imageformat_to_ext[fs.imageformat]
return DrawEigenLacing.get_eg2_image(
tree, (640, 480), ext,
v1, v2s,
fs.draw_background, fs.draw_vertices, fs.draw_labels)
except CairoUtil.CairoUtilError as e:
raise HandlingError(e)
def get_response_content(fs):
# get a properly formatted newick tree with branch lengths
tree_string = '((1:1, 2:1)6:1, 3:1, (4:1, 5:1)7:1)8;'
tree = Newick.parse(tree_string, SpatialTree.SpatialTree)
# get the fiedler-like vertex valuation
fiedler = [1, 1, -1, -1, -1, 1, -1, -1]
# create a node id map
ids = [None] * 8
for node in tree.preorder():
index = int(node.name) - 1
ids[index] = id(node)
# convert fiedler into a dictionary
v1 = dict((ids[i], float(fiedler[i])) for i in range(8))
# convert the annotations into dictionaries
v2s = [dict((ids[i], float(v[i])) for i in range(8)) for v in g_annotation]
# do the layout
try:
layout = FastDaylightLayout.StraightBranchLayout()
layout.do_layout(tree)
except RuntimeError as e:
pass
# draw the image
try:
ext = Form.g_imageformat_to_ext[fs.imageformat]
return DrawEigenLacing.get_eg2_image(tree, (640, 480), ext, v1, v2s,
fs.draw_background,
fs.draw_vertices, fs.draw_labels)
except CairoUtil.CairoUtilError as e:
raise HandlingError(e)
def get_response_content(fs):
# get a properly formatted newick tree with branch lengths
tree = Newick.parse(fs.tree, SpatialTree.SpatialTree)
# get the vertex valuations
id_to_v1 = Harmonic.get_harmonic_valuations(tree, fs.eig_idx1)
id_to_v2 = Harmonic.get_harmonic_valuations(tree, fs.eig_idx2)
# do the layout
try:
layout = FastDaylightLayout.StraightBranchLayout()
layout.do_layout(tree)
except RuntimeError as e:
pass
# draw the image
try:
ext = Form.g_imageformat_to_ext[fs.imageformat]
return DrawEigenLacing.get_single_tree_image(
tree, (640, 480), ext, id_to_v1, id_to_v2)
except CairoUtil.CairoUtilError as e:
raise HandlingError(e)
def draw_labels_ftree(T, N, context, v_to_location):
"""
Use degree anchors for label placement.
"""
for v in Ftree.T_to_order(T):
if v not in N:
continue
label = N[v]
# get the parameters for the label
theta = DrawEigenLacing.get_free_angle_ftree(T, v, v_to_location)
x, y = v_to_location[v]
# draw the text relative to the location
theta += math.pi
float_degree = ((theta % (2 * math.pi)) * 360) / (2 * math.pi)
degree = int(math.floor(float_degree))
#style = 'anchor=%s,inner sep=1pt' % degree
style = 'anchor=%s' % degree
context.add_line('\\node[%s] at (%.4f,%.4f) {%s};' %
(style, x, y, label))
def get_response_content(fs):
# get a properly formatted newick tree with branch lengths
tree = Newick.parse(fs.tree, SpatialTree.SpatialTree)
# get the vertex valuations
id_to_v1 = Harmonic.get_harmonic_valuations(tree, fs.eig_idx1)
id_to_v2 = Harmonic.get_harmonic_valuations(tree, fs.eig_idx2)
# do the layout
try:
layout = FastDaylightLayout.StraightBranchLayout()
layout.do_layout(tree)
except RuntimeError as e:
pass
# draw the image
try:
ext = Form.g_imageformat_to_ext[fs.imageformat]
return DrawEigenLacing.get_single_tree_image(tree, (640, 480), ext,
id_to_v1, id_to_v2)
except CairoUtil.CairoUtilError as e:
raise HandlingError(e)
def draw_labels_ftree(T, N, context, v_to_location):
"""
Use degree anchors for label placement.
"""
for v in Ftree.T_to_order(T):
if v not in N:
continue
label = N[v]
# get the parameters for the label
theta = DrawEigenLacing.get_free_angle_ftree(T, v, v_to_location)
x, y = v_to_location[v]
# draw the text relative to the location
theta += math.pi
float_degree = ((theta % (2 * math.pi)) * 360) / (2 * math.pi)
degree = int(math.floor(float_degree))
#style = 'anchor=%s,inner sep=1pt' % degree
style = 'anchor=%s' % degree
context.add_line(
'\\node[%s] at (%.4f,%.4f) {%s};' % (
style, x, y, label))
def get_response_content(fs):
# get a properly formatted newick tree with branch lengths
tree = Newick.parse(fs.tree, SpatialTree.SpatialTree)
# get the vertex valuations
valuations = [Harmonic.get_harmonic_valuations(
tree, i) for i in range(fs.first_index, fs.last_index+1)]
# do the layout
try:
layout = FastDaylightLayout.StraightBranchLayout()
layout.do_layout(tree)
except RuntimeError as e:
pass
# draw the image
try:
ext = Form.g_imageformat_to_ext[fs.imageformat]
return DrawEigenLacing.get_forest_image(
tree, (640, 480), ext, valuations,
fs.draw_background, fs.draw_vertices, fs.draw_labels)
except CairoUtil.CairoUtilError as e:
raise HandlingError(e)
def get_response_content(fs):
# get a properly formatted newick tree with branch lengths
tree = Newick.parse(fs.tree, SpatialTree.SpatialTree)
# get the vertex valuations
valuations = [
Harmonic.get_harmonic_valuations(tree, i)
for i in range(fs.first_index, fs.last_index + 1)
]
# do the layout
try:
layout = FastDaylightLayout.StraightBranchLayout()
layout.do_layout(tree)
except RuntimeError as e:
pass
# draw the image
try:
ext = Form.g_imageformat_to_ext[fs.imageformat]
physical_size = (fs.width, fs.height)
return DrawEigenLacing.get_forest_image_revised(
tree, physical_size, ext, valuations, fs.draw_background,
fs.draw_labels, fs.inner_margin, fs.outer_margin, fs.reflect_trees)
except CairoUtil.CairoUtilError as e:
raise HandlingError(e)